How do i align connected faces to axis?
I will post 2 ways to do that.



First way :         


Select inner circles which you are going to straighten, hit X and select Edgeloops.
Use loopcut tool Ctrl+R and increase loopcuts to 2. These new loopcuts are your recreated circles, straightened along the line between outer circles 


(Note that the angles of original circles if they were rotated aren't saved).



Second way:     

(this way is a little tricky) If you do want to preserve original inner circles and not recreating them, then:


Select outer circles, hit Ctrl+E and select Bridge Edge Loops.





Use loopcut tool Ctrl+R and make 1 loopcut on the created bridge between the outer circles. Place it roughly at the place you'd like one of the inner circles should be. 
Hit Shift+S and select Cursor To Selection. After that, while this created loopcut is still selected, hit X and select Edgeloop.





Select adjacent inner circle you are straightening, hit Shift+S and select Selection To Cursor (Offset). One of your inner circles is straightened now. 
Repeat that for another inner circle.





Select outer circles, hit X and select Faces. This will delete additional geometry created by Bridge Edge Loops.